Starting phenix.real_space_refine
on Fri Feb 14 04:48:07 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7zxt_15016/02_2025/7zxt_15016.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zxt_15016/02_2025/7zxt_15016.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zxt_15016/02_2025/7zxt_15016.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zxt_15016/02_2025/7zxt_15016.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zxt_15016/02_2025/7zxt_15016.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zxt_15016/02_2025/7zxt_15016.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      90      5.16       5
     C    6534      2.51       5
     N    1668      2.21       5
     O    1632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9924
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1654
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 4.29, per 1000 atoms: 0.43
  Number of scatterers: 9924
  At special positions: 0
  Unit cell: (105.294, 101.37, 91.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      90     16.00
     O    1632      8.00
     N    1668      7.00
     C    6534      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 168 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2376

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      72.4% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 10
    Processing helix  chain 'A' and resid 23 through 42
      removed outlier: 3.608A  pdb=" N   VAL A  27 " --> pdb=" O   VAL A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 72 through 107
      Proline residue:  A  87  - end of helix
    Processing helix  chain 'A' and resid 123 through 157
    Processing helix  chain 'A' and resid 183 through 220
    Processing helix  chain 'B' and resid 2 through 10
    Processing helix  chain 'B' and resid 23 through 42
      removed outlier: 3.608A  pdb=" N   VAL B  27 " --> pdb=" O   VAL B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 72 through 107
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 123 through 157
    Processing helix  chain 'B' and resid 183 through 220
    Processing helix  chain 'C' and resid 2 through 10
    Processing helix  chain 'C' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL C  27 " --> pdb=" O   VAL C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 72 through 107
      Proline residue:  C  87  - end of helix
    Processing helix  chain 'C' and resid 123 through 157
    Processing helix  chain 'C' and resid 183 through 220
    Processing helix  chain 'D' and resid 2 through 10
    Processing helix  chain 'D' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL D  27 " --> pdb=" O   VAL D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 69
    Processing helix  chain 'D' and resid 72 through 107
      Proline residue:  D  87  - end of helix
    Processing helix  chain 'D' and resid 123 through 157
    Processing helix  chain 'D' and resid 183 through 220
    Processing helix  chain 'E' and resid 2 through 10
    Processing helix  chain 'E' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL E  27 " --> pdb=" O   VAL E  23 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 59 through 69
    Processing helix  chain 'E' and resid 72 through 107
      Proline residue:  E  87  - end of helix
    Processing helix  chain 'E' and resid 123 through 157
    Processing helix  chain 'E' and resid 183 through 220
    Processing helix  chain 'F' and resid 2 through 10
    Processing helix  chain 'F' and resid 23 through 42
      removed outlier: 3.609A  pdb=" N   VAL F  27 " --> pdb=" O   VAL F  23 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 59 through 69
    Processing helix  chain 'F' and resid 72 through 107
      Proline residue:  F  87  - end of helix
    Processing helix  chain 'F' and resid 123 through 157
    Processing helix  chain 'F' and resid 183 through 220
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53
      removed outlier: 4.039A  pdb=" N   ILE A  52 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE A 180 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53
      removed outlier: 4.038A  pdb=" N   ILE B  52 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE B 180 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53
      removed outlier: 4.039A  pdb=" N   ILE C  52 " --> pdb=" O   PHE C 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE C 180 " --> pdb=" O   ILE C  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53
      removed outlier: 4.039A  pdb=" N   ILE D  52 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE D 180 " --> pdb=" O   ILE D  52 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53
      removed outlier: 4.038A  pdb=" N   ILE E  52 " --> pdb=" O   PHE E 180 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE E 180 " --> pdb=" O   ILE E  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53
      removed outlier: 4.038A  pdb=" N   ILE F  52 " --> pdb=" O   PHE F 180 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE F 180 " --> pdb=" O   ILE F  52 " (cutoff:3.500A)

    751 hydrogen bonds defined for protein.
    2235 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.82

  Time building geometry restraints manager: 2.95 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.35: 3006
        1.35 -     1.47: 2751
        1.47 -     1.60: 4293
        1.60 -     1.72: 0
        1.72 -     1.84: 132
  Bond restraints: 10182
  Sorted by residual:
  bond pdb=" C   THR B  86 "
       pdb=" N   PRO B  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.64e+00
  bond pdb=" C   THR E  86 "
       pdb=" N   PRO E  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.64e+00
  bond pdb=" C   THR F  86 "
       pdb=" N   PRO F  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.62e+00
  bond pdb=" C   THR D  86 "
       pdb=" N   PRO D  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.025 1.36e-02 5.41e+03 3.47e+00
  bond pdb=" C   THR C  86 "
       pdb=" N   PRO C  87 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.025 1.36e-02 5.41e+03 3.42e+00
  ... (remaining 10177 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 13433
        1.47 -     2.93: 331
        2.93 -     4.40: 54
        4.40 -     5.87: 30
        5.87 -     7.34: 12
  Bond angle restraints: 13860
  Sorted by residual:
  angle pdb=" N   ILE A  20 "
        pdb=" CA  ILE A  20 "
        pdb=" C   ILE A  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.02    4.10 8.40e-01 1.42e+00 2.38e+01
  angle pdb=" N   ILE D  20 "
        pdb=" CA  ILE D  20 "
        pdb=" C   ILE D  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.06    4.06 8.40e-01 1.42e+00 2.34e+01
  angle pdb=" N   ILE E  20 "
        pdb=" CA  ILE E  20 "
        pdb=" C   ILE E  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.06    4.06 8.40e-01 1.42e+00 2.34e+01
  angle pdb=" N   ILE C  20 "
        pdb=" CA  ILE C  20 "
        pdb=" C   ILE C  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.07    4.05 8.40e-01 1.42e+00 2.33e+01
  angle pdb=" N   ILE F  20 "
        pdb=" CA  ILE F  20 "
        pdb=" C   ILE F  20 "
      ideal   model   delta    sigma   weight residual
     112.12  108.07    4.05 8.40e-01 1.42e+00 2.33e+01
  ... (remaining 13855 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.98: 5377
       14.98 -    29.96: 432
       29.96 -    44.94: 127
       44.94 -    59.92: 7
       59.92 -    74.90: 6
  Dihedral angle restraints: 5949
    sinusoidal: 2295
      harmonic: 3654
  Sorted by residual:
  dihedral pdb=" CA  CYS E 179 "
           pdb=" C   CYS E 179 "
           pdb=" N   PHE E 180 "
           pdb=" CA  PHE E 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.79  -30.21     0      5.00e+00 4.00e-02 3.65e+01
  dihedral pdb=" CA  CYS B 179 "
           pdb=" C   CYS B 179 "
           pdb=" N   PHE B 180 "
           pdb=" CA  PHE B 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.79  -30.21     0      5.00e+00 4.00e-02 3.65e+01
  dihedral pdb=" CA  CYS F 179 "
           pdb=" C   CYS F 179 "
           pdb=" N   PHE F 180 "
           pdb=" CA  PHE F 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.81  -30.19     0      5.00e+00 4.00e-02 3.65e+01
  ... (remaining 5946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1157
       0.041 -    0.081: 399
       0.081 -    0.122: 64
       0.122 -    0.162: 6
       0.162 -    0.203: 18
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CB  VAL F  13 "
            pdb=" CA  VAL F  13 "
            pdb=" CG1 VAL F  13 "
            pdb=" CG2 VAL F  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  VAL D  13 "
            pdb=" CA  VAL D  13 "
            pdb=" CG1 VAL D  13 "
            pdb=" CG2 VAL D  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  VAL A  13 "
            pdb=" CA  VAL A  13 "
            pdb=" CG1 VAL A  13 "
            pdb=" CG2 VAL A  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG F 183 "    0.020 5.00e-02 4.00e+02   3.05e-02 1.48e+00
        pdb=" N   PRO F 184 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO F 184 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO F 184 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 183 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO A 184 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 184 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 184 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 183 "   -0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO C 184 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C 184 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 184 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 63
        2.60 -     3.18: 8746
        3.18 -     3.75: 16307
        3.75 -     4.33: 20356
        4.33 -     4.90: 34509
  Nonbonded interactions: 79981
  Sorted by model distance:
  nonbonded pdb=" SG  CYS D  64 "
            pdb=" SG  CYS D 168 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS F  64 "
            pdb=" SG  CYS F 168 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS C  64 "
            pdb=" SG  CYS C 168 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS E  64 "
            pdb=" SG  CYS E 168 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS B  64 "
            pdb=" SG  CYS B 168 "
     model   vdw
     2.029 3.760
  ... (remaining 79976 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.210
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10182  Z= 0.188
  Angle     :  0.626   7.337  13860  Z= 0.363
  Chirality :  0.043   0.203   1644
  Planarity :  0.003   0.030   1662
  Dihedral  : 12.065  74.901   3564
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.47 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.51 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.83 (0.24), residues: 1212
  helix:  3.93 (0.15), residues: 876
  sheet:  1.68 (0.55), residues: 60
  loop : -2.43 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  44 
 HIS   0.002   0.000   HIS C  97 
 PHE   0.008   0.001   PHE E  51 
 TYR   0.007   0.001   TYR B 135 
 ARG   0.002   0.000   ARG E  32 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.095 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 1.3067
  time to fit residues: 333.2791
Evaluate side-chains
  158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   chunk 50 optimal weight:   20.0000
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
B  99 GLN
D  97 HIS
E  99 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.091988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.063285 restraints weight = 20136.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 2.38
r_work: 0.2731 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.049  10182  Z= 0.526
  Angle     :  0.683  10.801  13860  Z= 0.361
  Chirality :  0.046   0.177   1644
  Planarity :  0.004   0.042   1662
  Dihedral  :  4.620  32.121   1350
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.38 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 15.59 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.03 (0.23), residues: 1212
  helix:  3.40 (0.15), residues: 876
  sheet: -0.28 (0.52), residues: 72
  loop : -2.57 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A  77 
 HIS   0.012   0.002   HIS B 123 
 PHE   0.014   0.002   PHE C  68 
 TYR   0.013   0.002   TYR E 151 
 ARG   0.003   0.001   ARG B  32 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 155
  time to evaluate  : 1.197 
Fit side-chains
REVERT: C  153 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8564 (t80)
REVERT: F  153 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8555 (t80)
  outliers start: 33
  outliers final: 16
  residues processed: 183
  average time/residue: 1.3822
  time to fit residues: 269.3980
Evaluate side-chains
  171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue  130 THR
Chi-restraints excluded: chain C residue  153 PHE
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  130 THR
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue  130 THR
Chi-restraints excluded: chain F residue  153 PHE
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  217 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 113 optimal weight:    0.7980
   chunk 69 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 61 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.097063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.068340 restraints weight = 20200.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.42
r_work: 0.2840 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10182  Z= 0.164
  Angle     :  0.529   7.399  13860  Z= 0.279
  Chirality :  0.039   0.154   1644
  Planarity :  0.003   0.017   1662
  Dihedral  :  3.883  28.612   1350
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  2.64 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.39 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.87 (0.24), residues: 1212
  helix:  4.03 (0.14), residues: 882
  sheet:  1.12 (0.50), residues: 60
  loop : -2.70 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 132 
 HIS   0.010   0.001   HIS B 123 
 PHE   0.011   0.001   PHE B  31 
 TYR   0.006   0.001   TYR E 211 
 ARG   0.003   0.000   ARG B  75 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 1.093 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8334 (m-30) cc_final: 0.8082 (m-30)
REVERT: A   99 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7728 (tm-30)
REVERT: B   66 ASP cc_start: 0.8227 (m-30) cc_final: 0.7983 (m-30)
REVERT: B   99 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7826 (tm-30)
REVERT: C   66 ASP cc_start: 0.8239 (m-30) cc_final: 0.7994 (m-30)
REVERT: D   66 ASP cc_start: 0.8357 (m-30) cc_final: 0.8094 (m-30)
REVERT: D   99 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7735 (tm-30)
REVERT: E   66 ASP cc_start: 0.8225 (m-30) cc_final: 0.7979 (m-30)
REVERT: F   66 ASP cc_start: 0.8247 (m-30) cc_final: 0.8010 (m-30)
  outliers start: 22
  outliers final: 6
  residues processed: 180
  average time/residue: 1.3294
  time to fit residues: 255.5862
Evaluate side-chains
  165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 159
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain B residue  126 HIS
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain D residue   46 ASP
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 115 optimal weight:    5.9990
   chunk 84 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.094848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.065794 restraints weight = 19932.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 2.41
r_work: 0.2793 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10182  Z= 0.246
  Angle     :  0.551   7.958  13860  Z= 0.294
  Chirality :  0.040   0.155   1644
  Planarity :  0.003   0.023   1662
  Dihedral  :  3.982  27.937   1350
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.56 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 19.46 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.63 (0.24), residues: 1212
  helix:  3.82 (0.15), residues: 882
  sheet:  1.36 (0.51), residues: 60
  loop : -2.75 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 132 
 HIS   0.002   0.001   HIS B  97 
 PHE   0.009   0.001   PHE B  68 
 TYR   0.010   0.001   TYR D 151 
 ARG   0.003   0.000   ARG B  75 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 1.134 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8317 (m-30) cc_final: 0.8113 (m-30)
REVERT: A   99 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7589 (tm130)
REVERT: A  219 ARG cc_start: 0.1897 (OUTLIER) cc_final: 0.0937 (ttt180)
REVERT: B   66 ASP cc_start: 0.8217 (m-30) cc_final: 0.7990 (m-30)
REVERT: B   99 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7595 (tm130)
REVERT: B  219 ARG cc_start: 0.1860 (OUTLIER) cc_final: 0.0882 (ttt180)
REVERT: C   66 ASP cc_start: 0.8197 (m-30) cc_final: 0.7951 (m-30)
REVERT: C  219 ARG cc_start: 0.2049 (OUTLIER) cc_final: 0.1084 (ttt180)
REVERT: D   66 ASP cc_start: 0.8326 (m-30) cc_final: 0.8100 (m-30)
REVERT: D   99 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7601 (tm130)
REVERT: D  219 ARG cc_start: 0.1874 (OUTLIER) cc_final: 0.0936 (ttt180)
REVERT: E   66 ASP cc_start: 0.8235 (m-30) cc_final: 0.8019 (m-30)
REVERT: E   99 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7565 (tm130)
REVERT: E  219 ARG cc_start: 0.1851 (OUTLIER) cc_final: 0.0855 (ttt180)
REVERT: F   66 ASP cc_start: 0.8213 (m-30) cc_final: 0.7973 (m-30)
REVERT: F  219 ARG cc_start: 0.2024 (OUTLIER) cc_final: 0.1067 (ttt180)
  outliers start: 22
  outliers final: 10
  residues processed: 182
  average time/residue: 1.3566
  time to fit residues: 263.6536
Evaluate side-chains
  170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 1.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 69 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 95 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.095750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.066792 restraints weight = 20099.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.44
r_work: 0.2817 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10182  Z= 0.199
  Angle     :  0.541   7.248  13860  Z= 0.290
  Chirality :  0.039   0.149   1644
  Planarity :  0.003   0.026   1662
  Dihedral  :  3.889  26.418   1350
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.39 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 20.72 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.67 (0.24), residues: 1212
  helix:  3.85 (0.15), residues: 882
  sheet:  1.51 (0.52), residues: 60
  loop : -2.75 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 132 
 HIS   0.003   0.001   HIS A 123 
 PHE   0.009   0.001   PHE E  31 
 TYR   0.008   0.001   TYR D 151 
 ARG   0.003   0.000   ARG B  75 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8272 (m-30) cc_final: 0.8041 (m-30)
REVERT: A   99 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7584 (tm130)
REVERT: A  219 ARG cc_start: 0.1917 (OUTLIER) cc_final: 0.0966 (ttt180)
REVERT: B   66 ASP cc_start: 0.8277 (m-30) cc_final: 0.8040 (m-30)
REVERT: B   99 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7602 (tm130)
REVERT: B  219 ARG cc_start: 0.1832 (OUTLIER) cc_final: 0.0863 (ttt180)
REVERT: C   66 ASP cc_start: 0.8203 (m-30) cc_final: 0.7943 (m-30)
REVERT: C  219 ARG cc_start: 0.2130 (OUTLIER) cc_final: 0.1181 (ttt180)
REVERT: D   66 ASP cc_start: 0.8332 (m-30) cc_final: 0.8086 (m-30)
REVERT: D   99 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7605 (tm130)
REVERT: D  219 ARG cc_start: 0.1898 (OUTLIER) cc_final: 0.0961 (ttt180)
REVERT: E   66 ASP cc_start: 0.8266 (m-30) cc_final: 0.8026 (m-30)
REVERT: E   99 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7610 (tm130)
REVERT: E  219 ARG cc_start: 0.1928 (OUTLIER) cc_final: 0.0937 (ttt180)
REVERT: F   66 ASP cc_start: 0.8250 (m-30) cc_final: 0.7988 (m-30)
REVERT: F  219 ARG cc_start: 0.2108 (OUTLIER) cc_final: 0.1157 (ttt180)
  outliers start: 19
  outliers final: 8
  residues processed: 169
  average time/residue: 1.4072
  time to fit residues: 252.9869
Evaluate side-chains
  166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 69 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN
F  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.095293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.066011 restraints weight = 20159.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 2.46
r_work: 0.2799 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10182  Z= 0.219
  Angle     :  0.556   7.447  13860  Z= 0.296
  Chirality :  0.039   0.149   1644
  Planarity :  0.003   0.029   1662
  Dihedral  :  3.900  25.992   1350
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.48 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 20.81 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.57 (0.24), residues: 1212
  helix:  3.76 (0.15), residues: 882
  sheet:  1.57 (0.53), residues: 60
  loop : -2.75 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 132 
 HIS   0.004   0.001   HIS B 123 
 PHE   0.008   0.001   PHE F  31 
 TYR   0.009   0.001   TYR B 151 
 ARG   0.003   0.000   ARG B  75 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 154
  time to evaluate  : 1.126 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8249 (m-30) cc_final: 0.8017 (m-30)
REVERT: A   99 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7444 (tm130)
REVERT: B   66 ASP cc_start: 0.8279 (m-30) cc_final: 0.8053 (m-30)
REVERT: B   99 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7532 (tm-30)
REVERT: C   66 ASP cc_start: 0.8212 (m-30) cc_final: 0.7956 (m-30)
REVERT: D   66 ASP cc_start: 0.8308 (m-30) cc_final: 0.8088 (m-30)
REVERT: D   99 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7457 (tm130)
REVERT: E   66 ASP cc_start: 0.8272 (m-30) cc_final: 0.8032 (m-30)
REVERT: E   99 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7527 (tm130)
REVERT: F   66 ASP cc_start: 0.8238 (m-30) cc_final: 0.7973 (m-30)
  outliers start: 18
  outliers final: 16
  residues processed: 163
  average time/residue: 1.3121
  time to fit residues: 229.2340
Evaluate side-chains
  165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 109 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.095362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.066180 restraints weight = 20314.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.46
r_work: 0.2815 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10182  Z= 0.220
  Angle     :  0.569   7.431  13860  Z= 0.302
  Chirality :  0.039   0.148   1644
  Planarity :  0.003   0.031   1662
  Dihedral  :  3.890  25.461   1350
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.48 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 21.80 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.56 (0.24), residues: 1212
  helix:  3.77 (0.15), residues: 882
  sheet:  1.52 (0.54), residues: 60
  loop : -2.81 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E 132 
 HIS   0.002   0.001   HIS B 123 
 PHE   0.009   0.001   PHE E  68 
 TYR   0.010   0.001   TYR E 151 
 ARG   0.002   0.000   ARG B  75 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 1.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8245 (m-30) cc_final: 0.8034 (m-30)
REVERT: A   99 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: A  219 ARG cc_start: 0.2102 (OUTLIER) cc_final: 0.1043 (ttt180)
REVERT: B   66 ASP cc_start: 0.8301 (m-30) cc_final: 0.8077 (m-30)
REVERT: B   99 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7632 (tm-30)
REVERT: B  219 ARG cc_start: 0.2026 (OUTLIER) cc_final: 0.1021 (ttt180)
REVERT: C   66 ASP cc_start: 0.8240 (m-30) cc_final: 0.7982 (m-30)
REVERT: C  219 ARG cc_start: 0.2181 (OUTLIER) cc_final: 0.1178 (ttt180)
REVERT: D   66 ASP cc_start: 0.8316 (m-30) cc_final: 0.8092 (m-30)
REVERT: D   99 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7514 (tm-30)
REVERT: D  219 ARG cc_start: 0.2064 (OUTLIER) cc_final: 0.1032 (ttt180)
REVERT: E   66 ASP cc_start: 0.8283 (m-30) cc_final: 0.8055 (m-30)
REVERT: E   99 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7107 (tm130)
REVERT: E  103 LYS cc_start: 0.8093 (ptpt) cc_final: 0.7842 (ptpt)
REVERT: E  219 ARG cc_start: 0.2120 (OUTLIER) cc_final: 0.1051 (ttt180)
REVERT: F   66 ASP cc_start: 0.8266 (m-30) cc_final: 0.8016 (m-30)
REVERT: F  219 ARG cc_start: 0.2202 (OUTLIER) cc_final: 0.1172 (ttt180)
  outliers start: 21
  outliers final: 17
  residues processed: 169
  average time/residue: 1.4540
  time to fit residues: 261.3772
Evaluate side-chains
  173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   46 ASP
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 30 optimal weight:   20.0000
   chunk 89 optimal weight:    8.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.093623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.064360 restraints weight = 20272.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 2.44
r_work: 0.2773 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10182  Z= 0.326
  Angle     :  0.622   8.665  13860  Z= 0.329
  Chirality :  0.041   0.156   1644
  Planarity :  0.004   0.033   1662
  Dihedral  :  4.098  25.470   1350
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  3.14 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 20.36 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.30 (0.24), residues: 1212
  helix:  3.53 (0.15), residues: 882
  sheet:  1.46 (0.54), residues: 60
  loop : -2.74 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  77 
 HIS   0.002   0.001   HIS B 123 
 PHE   0.010   0.002   PHE D  68 
 TYR   0.012   0.001   TYR E 151 
 ARG   0.003   0.000   ARG E  75 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 151
  time to evaluate  : 0.995 
Fit side-chains
REVERT: A   66 ASP cc_start: 0.8266 (m-30) cc_final: 0.8050 (m-30)
REVERT: A   99 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7587 (tm-30)
REVERT: A  219 ARG cc_start: 0.2161 (OUTLIER) cc_final: 0.1028 (ttt180)
REVERT: B   66 ASP cc_start: 0.8285 (m-30) cc_final: 0.8069 (m-30)
REVERT: B   99 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7596 (tm-30)
REVERT: B  219 ARG cc_start: 0.2086 (OUTLIER) cc_final: 0.0991 (ttt180)
REVERT: C   66 ASP cc_start: 0.8239 (m-30) cc_final: 0.8006 (m-30)
REVERT: C  219 ARG cc_start: 0.2090 (OUTLIER) cc_final: 0.1006 (ttt180)
REVERT: D   66 ASP cc_start: 0.8289 (m-30) cc_final: 0.8071 (m-30)
REVERT: D   99 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7598 (tm-30)
REVERT: D  219 ARG cc_start: 0.2126 (OUTLIER) cc_final: 0.1019 (ttt180)
REVERT: E   66 ASP cc_start: 0.8271 (m-30) cc_final: 0.8049 (m-30)
REVERT: E   99 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7564 (tm130)
REVERT: E  219 ARG cc_start: 0.2122 (OUTLIER) cc_final: 0.0988 (ttt180)
REVERT: F   66 ASP cc_start: 0.8251 (m-30) cc_final: 0.8002 (m-30)
REVERT: F  219 ARG cc_start: 0.2137 (OUTLIER) cc_final: 0.1047 (ttt180)
  outliers start: 45
  outliers final: 26
  residues processed: 185
  average time/residue: 1.3377
  time to fit residues: 263.9155
Evaluate side-chains
  177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 145
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  146 GLU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  146 GLU
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0270
   chunk 16 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 114 optimal weight:    4.9990
   chunk 118 optimal weight:    0.8980
   chunk 101 optimal weight:    7.9990
   chunk 106 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    0.6838

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.097534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.068337 restraints weight = 19924.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 2.49
r_work: 0.2856 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10182  Z= 0.171
  Angle     :  0.605   7.792  13860  Z= 0.318
  Chirality :  0.039   0.148   1644
  Planarity :  0.003   0.034   1662
  Dihedral  :  3.930  24.539   1350
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  2.64 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 22.16 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.76 (0.24), residues: 1212
  helix:  3.88 (0.15), residues: 882
  sheet:  1.43 (0.55), residues: 60
  loop : -2.57 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 132 
 HIS   0.002   0.000   HIS D  97 
 PHE   0.009   0.001   PHE B  31 
 TYR   0.012   0.001   TYR E 211 
 ARG   0.003   0.000   ARG F  22 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8226 (m-30) cc_final: 0.7982 (m-30)
REVERT: A  219 ARG cc_start: 0.2125 (OUTLIER) cc_final: 0.1109 (ttt180)
REVERT: B   66 ASP cc_start: 0.8335 (m-30) cc_final: 0.8100 (m-30)
REVERT: B   99 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7507 (tm-30)
REVERT: B  208 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8792 (mm-30)
REVERT: B  219 ARG cc_start: 0.2004 (OUTLIER) cc_final: 0.1007 (ttt180)
REVERT: C   66 ASP cc_start: 0.8262 (m-30) cc_final: 0.7979 (m-30)
REVERT: C  219 ARG cc_start: 0.2137 (OUTLIER) cc_final: 0.1179 (ttt180)
REVERT: D   66 ASP cc_start: 0.8320 (m-30) cc_final: 0.8082 (m-30)
REVERT: D  219 ARG cc_start: 0.2088 (OUTLIER) cc_final: 0.1089 (ttt180)
REVERT: E   66 ASP cc_start: 0.8319 (m-30) cc_final: 0.8082 (m-30)
REVERT: E   99 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7521 (tm-30)
REVERT: E  208 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8806 (mm-30)
REVERT: E  219 ARG cc_start: 0.2025 (OUTLIER) cc_final: 0.0978 (ttt180)
REVERT: F   66 ASP cc_start: 0.8305 (m-30) cc_final: 0.8024 (m-30)
REVERT: F  219 ARG cc_start: 0.2146 (OUTLIER) cc_final: 0.1166 (ttt180)
  outliers start: 22
  outliers final: 14
  residues processed: 175
  average time/residue: 1.4355
  time to fit residues: 267.1819
Evaluate side-chains
  163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  208 GLU
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   chunk 114 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
C  99 GLN
D  99 GLN
F  99 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.096205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.067157 restraints weight = 20199.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 2.47
r_work: 0.2834 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10182  Z= 0.217
  Angle     :  0.630   8.180  13860  Z= 0.331
  Chirality :  0.040   0.166   1644
  Planarity :  0.004   0.036   1662
  Dihedral  :  3.948  23.798   1350
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  3.05 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.98 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.76 (0.24), residues: 1212
  helix:  3.82 (0.15), residues: 882
  sheet:  1.56 (0.55), residues: 60
  loop : -2.37 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  44 
 HIS   0.001   0.001   HIS B 123 
 PHE   0.009   0.001   PHE B  31 
 TYR   0.014   0.001   TYR E 211 
 ARG   0.002   0.000   ARG E  75 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 149
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8227 (m-30) cc_final: 0.8002 (m-30)
REVERT: A  219 ARG cc_start: 0.2067 (OUTLIER) cc_final: 0.1058 (ttt180)
REVERT: B   66 ASP cc_start: 0.8326 (m-30) cc_final: 0.8092 (m-30)
REVERT: B  208 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8757 (mm-30)
REVERT: B  219 ARG cc_start: 0.2040 (OUTLIER) cc_final: 0.1058 (ttt180)
REVERT: C   66 ASP cc_start: 0.8218 (m-30) cc_final: 0.7976 (m-30)
REVERT: C  219 ARG cc_start: 0.2106 (OUTLIER) cc_final: 0.1137 (ttt180)
REVERT: D   66 ASP cc_start: 0.8307 (m-30) cc_final: 0.8081 (m-30)
REVERT: D  219 ARG cc_start: 0.2026 (OUTLIER) cc_final: 0.1052 (ttt180)
REVERT: E   66 ASP cc_start: 0.8307 (m-30) cc_final: 0.8072 (m-30)
REVERT: E   99 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7549 (tm-30)
REVERT: E  208 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8755 (mm-30)
REVERT: E  219 ARG cc_start: 0.2094 (OUTLIER) cc_final: 0.1071 (ttt180)
REVERT: F   66 ASP cc_start: 0.8247 (m-30) cc_final: 0.8004 (m-30)
REVERT: F  219 ARG cc_start: 0.2123 (OUTLIER) cc_final: 0.1127 (ttt180)
  outliers start: 29
  outliers final: 13
  residues processed: 167
  average time/residue: 1.4195
  time to fit residues: 252.0211
Evaluate side-chains
  157 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  219 ARG
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain D residue  219 ARG
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  208 GLU
Chi-restraints excluded: chain E residue  219 ARG
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  219 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 99 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0670
   chunk 59 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.8126

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.095264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.066064 restraints weight = 19955.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.47
r_work: 0.2809 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10182  Z= 0.255
  Angle     :  0.654   8.181  13860  Z= 0.345
  Chirality :  0.041   0.151   1644
  Planarity :  0.004   0.035   1662
  Dihedral  :  4.038  24.221   1350
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.14 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.25 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.71 (0.24), residues: 1212
  helix:  3.75 (0.15), residues: 882
  sheet:  1.63 (0.56), residues: 60
  loop : -2.27 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  44 
 HIS   0.002   0.001   HIS F  94 
 PHE   0.009   0.001   PHE E  68 
 TYR   0.017   0.001   TYR E 211 
 ARG   0.003   0.000   ARG E  75 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6362.79 seconds
wall clock time: 113 minutes 36.56 seconds (6816.56 seconds total)